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At least 37 records · Page 2Linked to original sources
USGS2024

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind. To that end, EEB is developing new tools to analyze the massive, complex, transdisciplinary datasets that result from such studies. The American Society for Microbiology’s Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the trajectory of EEB both within the Society and microbiology at large. Retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The retreat repeatedly emphasized that the future of science is through transdisciplinary collaborations that promote integration of diverse datasets and advanced technologies, while also genuinely fostering inclusivity, global collaborations, and public engagement. The American Society for Microbiology and EEB stand poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

mSphere↗
USGS2010

Ecological distribution and population physiology defined by proteomics in a natural microbial community

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ .

Molecular Systems Biology↗
USGS2015

Linking microbial community structure and microbial processes: An empirical and conceptual overview

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

FEMS Microbiology Ecology↗
USGS2004

Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates

Microorganisms play an important role in the weathering of silicate minerals in many subsurface environments, but an unanswered question is whether the mineral plays an important role in the microbial ecology. Silicate minerals often contain nutrients necessary for microbial growth, but whether the microbial community benefits from their release during weathering is unclear. In this study, we used field and laboratory approaches to investigate microbial interactions with minerals and glasses containing beneficial nutrients and metals. Field experiments from a petroleum-contaminated aquifer, where silicate weathering is substantially accelerated in the contaminated zone, revealed that phosphorus (P) and iron (Fe)-bearing silicate glasses were preferentially colonized and weathered, while glasses without these elements were typically barren of colonizing microorganisms, corroborating previous studies using feldspars. In laboratory studies, we investigated microbial weathering of silicates and the release of nutrients using a model ligand-promoted pathway. A metal-chelating organic ligand 3,4 dihydroxybenzoic acid (3,4 DHBA) was used as a source of chelated ferric iron, and a carbon source, to investigate mineral weathering rate and microbial metabolism. In the investigated aquifer, we hypothesize that microbes produce organic ligands to chelate metals, particularly Fe, for metabolic processes and also form stable complexes with Al and occasionally with Si. Further, the concentration of these ligands is apparently sufficient near an attached microorganism to destroy the silicate framework while releasing the nutrient of interest. In microcosms containing silicates and glasses with trace phosphate mineral inclusions, microbial biomass increased, indicating that the microbial community can use silicate-bound phosphate inclusions. The addition of a native microbial consortium to microcosms containing silicates or glasses with iron oxide inclusions correlated to accelerated weathering and release of Si into solution as well as the accelerated degradation of the model substrate 3,4 DHBA. We propose that silicate-bound P and Fe inclusions are bioavailable, and microorganisms may use organic ligands to dissolve the silicate matrix and access these otherwise limiting nutrients.

Chemical Geology↗
USGS2006

Mercury in water and biomass of microbial communities in hot springs of Yellowstone National Park, USA

Ultra-clean sampling methods and approaches typically used in pristine environments were applied to quantify concentrations of Hg species in water and microbial biomass from hot springs of Yellowstone National Park, features that are geologically enriched with Hg. Microbial populations of chemically-diverse hot springs were also characterized using modern methods in molecular biology as the initial step toward ongoing work linking Hg speciation with microbial processes. Molecular methods (amplification of environmental DNA using 16S rDNA primers, cloning, denatured gradient gel electrophoresis (DGGE) screening of clone libraries, and sequencing of representative clones) were used to examine the dominant members of microbial communities in hot springs. Total Hg (THg), monomethylated Hg (MeHg), pH, temperature, and other parameters influential to Hg speciation and microbial ecology are reported for hot springs water and associated microbial mats.

Applied Geochemistry↗
USGS2010

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

Ecosystems↗
USGS2005

Microbial responses and nitrous oxide emissions during wetting and drying of organically and conventionally managed soil under tomatoes

The types and amounts of carbon (C) and nitrogen (N) inputs, as well as irrigation management are likely to influence gaseous emissions and microbial ecology of agricultural soil. Carbon dioxide (CO2) and nitrous oxide (N2O) efflux, with and without acetylene inhibition, inorganic N, and microbial biomass C were measured after irrigation or simulated rainfall in two agricultural fields under tomatoes (Lycopersicon esculentum). The two fields, located in the California Central Valley, had either a history of high organic matter (OM) inputs ("organic" management) or one of low OM and inorganic fertilizer inputs ("conventional" management). In microcosms, where short-term microbial responses to wetting and drying were studied, the highest CO2 efflux took place at about 60% water-filled pore space (WFPS). At this moisture level, phospholipid fatty acids (PLFA) indicative of microbial nutrient availability were elevated and a PLFA stress indicator was depressed, suggesting peak microbial activity. The highest N 2O efflux in the organically managed soil (0.94 mg N2O-N m-2 h-1) occurred after manure and legume cover crop incorporation, and in the conventionally managed soil (2.12 mg N2O-N m-2 h-1) after inorganic N fertilizer inputs. Elevated N2O emissions occurred at a WFPS >60% and lasted <2 days after wetting, probably because the top layer (0-150 mm) of this silt loam soil dried quickly. Therefore, in these cropping systems, irrigation management might control the duration of elevated N2O efflux, even when C and inorganic N availability are high, whereas inorganic N concentrations should be kept low during times when soil moisture cannot be controlled.

Biology and Fertility of Soils↗
USGS2018

Understanding how microbiomes influence the systems they inhabit

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Nature Microbiology↗
USGS2012

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.

Microbiology and Molecular Biology Reviews↗
USGS2020

Compositional analysis of formation water geochemistry and microbiology of commercial and carbon dioxide-rich wells in the southwestern United States

Studies of naturally occurring subsurface carbon dioxide (CO 2 ) accumulations can provide useful information for potential CO 2 injection projects; however, the microbial communities and formation water geochemistry of most reservoirs are understudied. Formation water and microbial biomass were sampled at four CO 2 -rich reservoir sites: two within Bravo Dome, a commercial CO 2 field in New Mexico; one northwest of Bravo Dome in Colorado (Oakdale Field); and one southwest of Bravo Dome in New Mexico (Rafter “K” Ranch). Aside from the Rafter “K” Ranch site, minor differences were observed in the geochemistry of formation water collected from these sites compared to historical data. No organisms were significantly associated with Oakdale Field compared to the other three sites, nor were any hydrogeochemical or gas geochemical parameters (for example, CO 2 concentration) found to have significant associations with the microbial ecology of these four sites. Microorganisms from these sites were metabolically diverse and had the potential to (1) generate methane, (2) produce corrosive hydrogen sulfide (H 2 S), and (3) rapidly biofoul and (or) clog pore spaces by shifting microbial communities with changes in salinity or nutrient supply. This study demonstrates that high concentrations of CO 2 in subsurface reservoirs apparently have not imparted a distinct geochemical or microbiological signature on the associated formation waters and that the microorganisms in these reservoirs are metabolically diverse and could adapt to geochemical changes in the subsurface.

Colorado, New Mexico, Texas, Oklahoma↗
USGS2012

ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arx A was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arx A-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.

Environmental Microbiology↗
USGS2025

Hydraulic connectivity and hydrochemistry influence microbial community structure in agriculturally-affected alluvial aquifers in the Midwestern United States

Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination ( R 2 ) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae . Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae . Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.

Iowa, Minnesota↗
USGS2002

Microbial transformation of elements: The case of arsenic and selenium

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.

International Microbiology↗
USGS2007

Biogeochemistry of aquifer systems

Many studies have examined the differences in bacterial numbers, composition, and activity between groundwater and sediment samples. The majority of the literature has suggested higher percentages of attached bacteria than of unattached bacteria in aquifer systems, including in pristine aquifers and in aquifers contaminated with petroleum, creosote, sewage, and landfill leachate. In studies of aquifer biogeochemistry, much useful information regarding the microbial ecology of the system can be obtained by looking at organic compound and electron acceptor concentrations. An overview of approaches for identifying the redox characteristics of sediment is given in Christensen et al., and methods specific for determining reactive iron species in aquifers are reviewed by Heron et al. and Tuccillo et al. Other solid-phase electron acceptors that are important in aquifer systems include Mn(IV) oxides and barite. Important biogeochemical reactions catalyzed by indigenous microorganisms also are studied using a variety of experimental approaches including laboratory batch and column experiments as well as field-based in situ microcosms, tracer tests, and push-pull tests. The advantage of using a radiolabeled tracer in a study was that the reaction rates could be determined for the different steps in the denitrification pathway. Historically, researchers trained in geochemistry and hydrology created and tested hypotheses about aquifer biogeochemistry through laboratory assays and field-based geo-chemical measurements and experiments. Jeon et al. extended this research by using push-pull tests combined with stable-isotope probing to identify the specific members of the microbial community actively degrading naphthalene and rates of naphthalene degradation.

Book chapter↗
USGS1998

Using transport model interpretations of tracer tests to study microbial processes in groundwater

It has long been known that microorganisms affect the geochemistry of groundwater. But despite this recognition, little detailed information is available regarding the rates and the factors controlling microbial processes in groundwater. Part of the reason stems from the relatively inaccessible nature of most groundwater and the difficulties encountered in obtaining representative samples of groundwater and subsurface sediments. At the same time, most groundwater systems are nutrient poor or oligotrophic environments in which the resident microorganisms are severely stressed and often nearly inactive. These populations are functioning so slowly that many types of activity measurements designed to assess microbial processes in more productive environments are ineffective for groundwater. However, because groundwater is by far the largest reservoir of freshwater in the world ( Freeze and Cherry 1979 ), our lack of knowledge about groundwater microorganisms and their processes represents a significant void in the study of microbial ecology and in our ability to predict the outcome when these reserves are compromised by contamination.

Book chapter↗
USGS2000

Microbial control of mineral–groundwater equilibria: Macroscale to microscale

Using field and laboratory experiments, the geomicrobiology of a petroleum-contaminated aquifer and the relationship between mineral alteration, groundwater chemistry, and microbial colonization were examined. Results indicate that indigenous microorganisms influence mineral weathering at two scales of interaction: macroscale processes that perturb general groundwater chemistry and therefore mineralwater equilibria; and microscale interactions, where attached organisms locally perturb mineral±water equilibria, potentially releasing limiting trace nutrients from the dissolving mineral. In the contaminated unconfined glacio-fluvial aquifer near Bemidji, Minnesota, USA, carbonate chemistry is influenced primarily at the macroscale. Under oxic conditions, respiration by native aerobic heterotrophs produces excess carbon dioxide that promotes calcite and dolomite dissolution. Aerobic microorganisms do not colonize dolomite surfaces and few occur on calcite. Within the anoxic groundwater, calcite overgrowths form on uncolonized calcite cleavage surfaces, possibly due to the consumption of acidity by dissimilatory iron-reducing bacteria. As molecular oxygen concentration increases downgradient of the oil pool, aerobes again dominate and residual hydrocarbons and ferrous iron are oxidized, resulting in macroscale carbonate-mineral dissolution and iron precipitation. Feldspars, in contrast, weather exclusively at the microscale near attached microorganisms, principally in the anoxic region of the plume. Native organisms preferentially colonize feldspars that contain trace phosphorus as apatite inclusions, apparently as a consequence of the low P concentration in the groundwater. These feldspars weather rapidly, whereas nearby feldspars without trace P are uncolonized and unweathered. Feldspar dissolution is accompanied by the precipitation of secondary minerals, sometimes on the bacterial cell wall itself. These observations suggest a tightly linked biogeochemical system whereby microbial processes control mineral diagenesis at many scales of interaction, and the mineralogy and mineral chemistry influence microbial ecology. Only the macroscale interaction, however, is easily observable by standard geochemical methods, and documentation of the microscale interactions requires microscopic examination of microorganisms on mineral surfaces and the locally intense diagenetic reactions that result.

Hydrogeology Journal↗
USGS2008

Stress tolerance in plants via habitat-adapted symbiosis

We demonstrate that native grass species from coastal and geothermal habitats require symbiotic fungal endophytes for salt and heat tolerance, respectively. Symbiotically conferred stress tolerance is a habitat-specific phenomenon with geothermal endophytes conferring heat but not salt tolerance, and coastal endophytes conferring salt but not heat tolerance. The same fungal species isolated from plants in habitats devoid of salt or heat stress did not confer these stress tolerances. Moreover, fungal endophytes from agricultural crops conferred disease resistance and not salt or heat tolerance. We define habitat-specific, symbiotically-conferred stress tolerance as habitat-adapted symbiosis and hypothesize that it is responsible for the establishment of plants in high-stress habitats. The agricultural, coastal and geothermal plant endophytes also colonized tomato (a model eudicot) and conferred disease, salt and heat tolerance, respectively. In addition, the coastal plant endophyte colonized rice (a model monocot) and conferred salt tolerance. These endophytes have a broad host range encompassing both monocots and eudicots. Interestingly, the endophytes also conferred drought tolerance to plants regardless of the habitat of origin. Abiotic stress tolerance correlated either with a decrease in water consumption or reactive oxygen sensitivity/generation but not to increased osmolyte production. The ability of fungal endophytes to confer stress tolerance to plants may provide a novel strategy for mitigating the impacts of global climate change on agricultural and native plant communities.The ISME Journal (2008) 2, 404-416; doi:10.1038/ismej.2007.106; published online 7 February 2008. ?? 2008 International Society for Microbial Ecology All rights reserved.

ISME Journal↗
USGS2005

Whither or wither geomicrobiology in the era of 'community metagenomics'

Molecular techniques are valuable tools that can improve our understanding of the structure of microbial communities. They provide the ability to probe for life in all niches of the biosphere, perhaps even supplanting the need to cultivate microorganisms or to conduct ecophysiological investigations. However, an overemphasis and strict dependence on such large information-driven endeavours as environmental metagenomics could overwhelm the field, to the detriment of microbial ecology. We now call for more balanced, hypothesis-driven research efforts that couple metagenomics with classic approaches.

Nature Reviews Microbiology↗